Variant report

Variant	rs7123985
Chromosome Location	chr11:73260463-73260464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1002126	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1002127	1.00[CEU][hapmap]
rs10501411	0.89[CEU][hapmap]
rs11235738	1.00[JPT][hapmap]
rs11235745	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11235759	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11235770	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs11235775	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235809	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820577	0.82[EUR][1000 genomes]
rs11820929	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11821094	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11822984	0.82[EUR][1000 genomes]
rs11823913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11823923	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11824614	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11826896	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11826909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12269884	1.00[JPT][hapmap]
rs12274589	1.00[JPT][hapmap]
rs12276892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12277924	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282790	1.00[JPT][hapmap]
rs12285885	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12290623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs12290701	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290785	0.82[EUR][1000 genomes]
rs12290835	1.00[JPT][hapmap]
rs17132115	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244596	1.00[CEU][hapmap]
rs17244602	1.00[CEU][hapmap]
rs17244616	1.00[CEU][hapmap]
rs17310361	1.00[CEU][hapmap]
rs17310374	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17851510	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap]
rs1938777	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2298469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2298807	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3825005	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3933402	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs56884659	0.82[EUR][1000 genomes]
rs58573166	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59806295	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60860405	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61516411	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7101561	0.80[EUR][1000 genomes]
rs7101831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7110369	0.89[CEU][hapmap]
rs7114009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs7114376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115055	1.00[CEU][hapmap]
rs7118982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7122825	0.89[CEU][hapmap]
rs7125598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs7129990	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs7131383	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7131397	1.00[JPT][hapmap]
rs724111	1.00[CEU][hapmap]
rs73546720	0.82[EUR][1000 genomes]
rs73546735	0.82[EUR][1000 genomes]
rs73548680	0.82[EUR][1000 genomes]
rs73548688	0.82[EUR][1000 genomes]
rs7925226	1.00[CEU][hapmap]
rs7927344	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930454	0.89[CEU][hapmap]
rs7930880	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7934218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935948	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938391	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941359	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7944346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945825	1.00[CEU][hapmap]
rs7950375	0.82[EUR][1000 genomes]
rs7951072	1.00[CEU][hapmap]
rs7952686	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs876480	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs880317	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs947837	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9888218	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1048171	chr11:73210060-73271831	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7123985	P2RY2	cis	cerebellum	SCAN
rs7123985	ARHGEF17	cis	Whole Blood	GTEx
rs7123985	CCND1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73243400-73279600	Weak transcription	Fetal Stomach	stomach
2	chr11:73243800-73263000	Weak transcription	Fetal Intestine Small	intestine
3	chr11:73249600-73266000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr11:73249600-73266400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:73249600-73276000	Weak transcription	Fetal Muscle Leg	muscle
6	chr11:73249800-73262600	Weak transcription	Brain Anterior Caudate	brain
7	chr11:73250000-73261800	Weak transcription	Brain Substantia Nigra	brain
8	chr11:73250000-73262200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:73250000-73262600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:73250000-73262600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:73250000-73262800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:73250000-73265800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr11:73250000-73307800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:73250200-73266400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:73250200-73278800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:73250800-73262200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:73250800-73265800	Weak transcription	Right Atrium	heart
18	chr11:73250800-73282800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:73251000-73265600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:73251000-73288800	Weak transcription	Thymus	Thymus
21	chr11:73251200-73263000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:73251600-73262200	Weak transcription	Right Ventricle	heart
23	chr11:73251600-73262400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:73251600-73266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:73252000-73261200	Weak transcription	Dnd41	blood
26	chr11:73253600-73265800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:73253800-73262000	Weak transcription	Brain Angular Gyrus	brain
28	chr11:73253800-73307000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:73254000-73262200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:73257600-73266000	Weak transcription	Left Ventricle	heart
31	chr11:73258600-73266000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:73258800-73278000	Weak transcription	Primary B cells from cord blood	blood
33	chr11:73259800-73265600	Weak transcription	GM12878-XiMat	blood
34	chr11:73260000-73262200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:73260000-73265200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr11:73260200-73260600	Weak transcription	Monocytes-CD14+_RO01746	blood

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